Preparation of DNA Nanostructures with Repetitive Binding Motifs by Rolling Circle Amplification

Methods in Molecular Biology

Volumn 749, Issue , 2011, Pages 151-168

  Reiß, Edda ^a   Hölzel, Ralph ^b   Bier, Frank F ^b  

^a FRAUNHOFER INSTITUTE FOR BIOMEDICAL ENGINEERING   (Germany)

^b NONE

Author keywords

DNA nanostructure; Fluorescence microscopy; Phi29 DNA polymerase; Rolling circle amplification; Single stranded DNA; SYBR Green II

Indexed keywords

CIRCULAR DNA; DNA DIRECTED DNA POLYMERASE; NANOMATERIAL; ORGANIC COMPOUND; SINGLE STRANDED DNA; SYBR GREEN II;

ARTICLE; BACILLUS PHAGE; CHEMISTRY; ENZYMOLOGY; FLUORESCENCE MICROSCOPY; METABOLISM; METHODOLOGY; NANOTECHNOLOGY; NUCLEIC ACID AMPLIFICATION; NUCLEIC ACID HYBRIDIZATION;

BACILLUS PHAGES; DNA, CIRCULAR; DNA, SINGLE-STRANDED; DNA-DIRECTED DNA POLYMERASE; MICROSCOPY, FLUORESCENCE; NANOSTRUCTURES; NANOTECHNOLOGY; NUCLEIC ACID AMPLIFICATION TECHNIQUES; NUCLEIC ACID HYBRIDIZATION; ORGANIC CHEMICALS;

EID: 84855174477     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-142-0_11     Document Type: Chapter

References (18)

1. Fire, A., and Xu, S. Q. (1995) Rolling replication of short DNA circles Proc. Natl. Acad. Sci. U. S. A. 92, 4641–5.
2. Liu, D., Daubendiek, S. L., Zillman, M. A., Ryan, K., and Kool, E. T. (1996) Rolling circle DNA synthesis: Small circular oligonucleotides as efficient templates for DNA polymerases J. Am. Chem. Soc. 118, 1587–94.
3. Lizardi, P. M., Huang, X., Zhu, Z., Bray-Ward, P., Thomas, D. C., and Ward, D. C. (1998) Mutation detection and single-molecule counting using isothermal rolling-circle amplification Nat. Genet. 19, 225–32.
4. Schweitzer, B., Roberts, S., Grimwade, B., Shao, W., Wang, M., Fu, Q., Shu, Q., Laroche, I., Zhou, Z., Tchernev, V. T., Christiansen, J., Velleca, M., and Kingsmore, S., F. (2002) Muliplexed protein profiling on microarrays by rolling-circle amplification Nat. Biotechnol. 20, 359–65.
5. Beyer, S., Nickels, P., and Simmel, F. C. (2005) Periodic DNA nanotemplates synthesized by rolling circle amplification Nano Lett. 5, 719–22.
6. Deng, Z., Tian, Y., Lee, S. H., Ribbe, A. E., and Mao, C. (2005) DNA-encoded self-assembly of gold nanoparticles into one-dimensional arrays Angew. Chem., Int. Ed. 44, 3582–5.
7. Zhao, W., Gao, Y., Kandadai, S. A., Brook, M. A., and Li, Y. (2006) DNA polymerization on gold nanoparticles through rolling circle amplification: Towards novel scaffolds for three-dimensional periodic nanoassemblies Angew. Chem., Int. Ed. 45, 2409–13.
8. Cheglakov, Z., Weizmann, Y., Braunschweig, A. B., Wilner, O. I., and Willner, I. (2008) Increasing the complexity of periodic protein nanostructures by the rolling-circle-amplified synthesis of aptamers Angew Chem., Int. Ed. 47, 126–30.
9. Zhao, W., Ali, M. M., Brook, M. A., and Li, Y. (2008) Rolling circle amplification: Applications in nanotechnology and biodetection with functional nucleic acids Angew. Chem., Int. Ed. 47, 6330–7.
10. Reiß, E., Hölzel, R., Nickisch-Rosenegk, M. v., and Bier, F. F. (2006) Rolling circle amplification for spatially directed synthesis of a solid phase anchored single-stranded DNA molecule, in DNA-Based Nanoscale Integration: International Symposium on DNA-Based Nanoscale Integration, Jena, Germany 18–20 May 2006 (Fritzsche, W., ed.) 2006, AIP Conference Proceedings 859, American Institute of Physics, Melville, NY, pp. 25–30.
11. Frieden, M., Pedroso, E., and Kool, E. T. (1999) Tightening the belt on polymerases: Evaluating the physical constraints on enzyme substrate size Angew. Chem., Int. Ed. 38, 3654–7.
12. Diegelman, A. M., and Kool, E. T. (2001) Chemical and enzymatic methods for preparing circular single-stranded DNAs Curr Protoc Nucleic Acid Chem Chapter 5, Unit 5.2.
13. Epicentre Biotechnologies. Protocol for CircLigase™ ssDNA Ligase (continued Lit. #222) [homepage on the Internet]. No date [cited 2009 Jan 15]. Available from: http://www.epibio.com/litindex.asp.
14. Blanco, L., Bernad, A., Lázaro, J. M., Martín, G., Garmendia, C., and Salas, M. (1989) Highly efficient DNA synthesis by the phage Phi 29 DNA polymerase. Symmetrical mode of DNA replication J. Biol. Chem. 264, 8935–40.
15. Reiß, E., Hölzel, R., and Bier, F. F. (2009) Synthesis and stretching of rolling circle amplification products in a flow-through system Small 5, 2316–22.
16. Feldkamp, U., Schroeder, H., and Niemeyer, C. M. (2006) Design and evaluation of single-stranded DNA carrier molecules for DNA-directed assembly J. Biomol. Struct. Dyn. 23, 657–66.
17. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., and Struhl, K., (Eds.) (1999) Short Protocols in Molecular Biology 4th ed., John Wiley & Sons, USA.
18. Dean, F. B., Nelson, J. R., Giesler, T. L., and Lasken, R. S. (2001) Rapid amplification of plasmid and phage DNA using Phi29 DNA polymerase and multiply-primed rolling circle amplification Genome Res. 11, 1095–9.